repMeans: Compute mean of replicated spots

In MKmisc: Miscellaneous Functions from M. Kohl

Compute mean of replicated spots

Description

Compute mean of replicated spots where additionally spot flags may incorporated.

Usage

repMeans(x, flags, use.flags = NULL, ndups, spacing, method, ...)

Arguments

x	matrix or data.frame of expression values
flags	matrix or data.frame of spot flags; must have same dimension as x
use.flags	should flags be included and in which way; cf. section details
ndups	integer, number of replicates on chip. The number of rows of x must be divisible by ndups
spacing	the spacing between the rows of 'x' corresponding to replicated spots, spacing = 1 for consecutive spots; cf. function unwrapdups in package "limma"
method	function to aggregate the replicated spots. If missing, the mean is used.
...	optional arguments to method.

Details

The incorporation of spot flags is controlled via argument use.flags.

NULL: flags are not used; minimum flag value of replicated spots is returned

"max": only spots with flag value equal to the maximum flag value of replicated spots are used

"median": only spots with flag values larger or equal to median of replicated spots are used

"mean": only spots with flag values larger or equal to mean of replicated spots are used

Value

LIST with components

exprs	mean of expression values
flags	flags for mean expression values

Note

A first version of this function appeared in package SLmisc.

Author(s)

Matthias Kohl [e-mail]

See Also

unwrapdups

Examples

## only a dummy example
M <- matrix(rnorm(1000), ncol = 10)
FL <- matrix(rpois(1000, lambda = 10), ncol = 10) # only for this example
res <- repMeans(x = M, flags = FL, use.flags = "max", ndups = 5, spacing = 20)

MKmisc documentation built on Nov. 20, 2022, 1:05 a.m.